Josh Johnson is the 49ers’ only backup option beside Gabbert, and he made a valiant bid to stick on the roster. Johnson threw three touchdown passes, including one on his first snap, a 13-yard throw to Bruce Ellington with 34 seconds left in the first half.

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Safely watching from the sideline was Kaepernick, who coach Jim Harbaugh said Monday would start, like last year’s exhibition finale.

Kaepernick warmed up and stayed in full uniform, as did most other projected starters for the Sept. 7 regular-season opener, just up Interstate 45 against the Dallas Cowboys.

While Gabbert’s grasp on the No. 2 job could be best tied to his $2 million guaranteed salary, Thursday’s audition brought back reminders of his struggles in the first two exhibitions, not to mention his former tenure with the Jacksonville Jaguars.

Gabbert was 1-of-6 for 11 yards before throwing into double coverage and finding Derek Carrier for a 32-yard completion.

His overall exhibition stats: 22-of-47 for 186 yards, two touchdowns, two interceptions and a 54.0 passer rating.

Harbaugh hasn’t wavered on Gabbert as his No. 2 quarterback, though the coach threw open the job to anyone who didn’t commit a turnover after Gabbert, Johnson and McLeod Bethel-Thompson each committed one in an Aug. 17 loss to the Denver Broncos.

Gabbert struggled out of the gate against a Texans defense that sat all but three of its first-string players, including J.J. Watt, Jadeveon Clowney, Brian Cushing and Johnathan Joseph.

Gabbert overthrew Stevie Johnson on his first two pass attempts, and on the next possession, he had a third-down pass nearly intercepted after it sailed over 6-foot-4 tight end Vance McDonald. The third series stalled near the 49ers goal line, keyed by a holding penalty on Daniel Kilgore and a sack of Gabbert that left tackle Carter Bykowski allowed.

At least three of Gabbert’s passes went off receivers hands, those of Johnson, Ellington and Alfonso Smith. Gabbert showed his running ability more than he had, producing two carries for 11 yards and having one scramble wiped out by an in-the-grasp call.

Johnson completed his first four passes (for 49 yards) before Lance Lewis dropped a third-down pass. Johnson’s mobility also is a plus for his bid, and he used that to dash 17 yards on a fourth-and-2 keeper.

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Although Johnson had a third-quarter pass intercepted and returned for a touchdown (by Andre Hall), that blame can at least partly go to wideout L’Damian Washington, who whiffed on the ball. Johnson later found Kyle Nelson for a fourth-quarter touchdown pass.

No matter how well Johnson played Thursday, history shows it may not matter. He excelled in the 2012 exhibition finale but lost out on the No.3 role to Scott Tolzien. Johnson’s progress and Gabbert’s struggles could prompt the 49ers to carry three quarterbacks, something they did only part of last season.

— General manager Trent Baalke expects the NFL to announce potential discipline of linebacker Aldon Smith prior to Saturday, when teams must trim their roster to the 53-man limit. Smith would not count against that roster if he’s suspended for the start of the season, freeing up a spot for another player. Smith met with NFL commissioner Roger Goodell three weeks ago.

— Draft picks Dontae Johnson (fourth round) and Kenneth Acker (sixth round) likely have played their way onto the cornerback unit. That could jeopardize a spot for Chris Cook, a fifth-year veteran who started Thursday opposite Darryl Morris.

Cook made an interception 42 seconds before halftime. Neither Johnson nor Acker are expected to go unclaimed if the 49ers waive them in hopes of re-signing them to the 10-man practice squad Sunday.

— Kilgore, right guard Joe Looney and nose tackle Ian Williams were the only probable opening-day starters who played against the Texans.

— Kaepernick’s exhibition season consisted of seven series, only two of which resulted in scoring drives (two field goals). He had a 69.3 rating on 12-of-22 passing for 115 yards with no touchdowns or interceptions.

— Tight end Derek Carrier aggravated a hamstring injury and didn’t play after halftime.

— Johnson had no receptions Thursday and caught just 2-of-7 passes targeted for him (for 11 yards) in the exhibition season. He was acquired in a draft-day trade and has figured to at least rotate as the No. 3 wideout this season.

— Veteran wideout Brandon Lloyd did not play for the third time in four exhibitions, presumably because of an undisclosed injury. He had one reception for 7 yards in the game he played, against Denver.

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Gabbert is truly pressing during the game and looked terrible again.
I feel bad for the guy but he hasn’t proved to be on this Niner team, or any team for what if matters.
The Jags get the last laugh on us.